Chemical Components in the PDB

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A1AKG : Summary

Code

A1AKG

One-letter code

X

Molecule name

(3R)-3-(pyridin-4-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R)-3-(pyridin-4-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid
OpenEye OEToolkits 2.0.7 (3~{S})-3-pyridin-4-yl-3-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylcarbonylamino)propanoic acid

Formula

C15 H13 N5 O3

Formal charge

0

Molecular weight

311.295 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC(NC(=O)c1ncnc2[NH]ccc12)c1ccncc1
SMILES CACTVS 3.385 OC(=O)C[CH](NC(=O)c1ncnc2[nH]ccc12)c3ccncc3
SMILES OpenEye OEToolkits 2.0.7 c1c[nH]c2c1c(ncn2)C(=O)NC(CC(=O)O)c3ccncc3
Canonical SMILES CACTVS 3.385 OC(=O)C[C@H](NC(=O)c1ncnc2[nH]ccc12)c3ccncc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1c[nH]c2c1c(ncn2)C(=O)N[C@@H](CC(=O)O)c3ccncc3

IUPAC InChI

InChI=1S/C15H13N5O3/c21-12(22)7-11(9-1-4-16-5-2-9)20-15(23)13-10-3-6-17-14(10)19-8-18-13/h1-6,8,11H,7H2,(H,20,23)(H,21,22)(H,17,18,19)/t11-/m1/s1

IUPAC InChI key

HCKDZPDKIDVDLJ-LLVKDONJSA-N
A1AKG

wwPDB Information

Atom count

36 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2024-04-03

Last modified at

2024-05-10

Status

Released

Obsoleted

Not Assigned



A1AKG : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -1.878 -0.856 -1.462
2 N3 N N2 N Y N 0 -5.104 0.69 0.449
3 C4 C C1 N Y N 0 -1.756 -0.263 -0.275
4 C5 C C2 N Y N 0 -3.05 -0.959 -2.054
5 C6 C C3 N Y N 0 -4.149 0.115 -0.345
6 C7 C C4 N Y N 0 -4.531 1.181 1.591
7 C8 C C5 N Y N 0 -3.207 0.946 1.579
8 C10 C C6 N Y N 0 2.49 0.931 0.027
9 C13 C C7 N Y N 0 2.769 2.713 -1.537
10 O2 O O1 N N N 0 -0.343 0.395 1.469
11 C3 C C8 N N N 0 -0.436 -0.149 0.386
12 C9 C C9 N Y N 0 -2.912 0.25 0.331
13 N2 N N3 N Y N 0 -4.162 -0.492 -1.523
14 N N N4 N N N 0 0.663 -0.649 -0.213
15 C2 C C10 S N N 0 1.983 -0.442 0.388
16 C1 C C11 N N N 0 2.955 -1.499 -0.14
17 C C C12 N N N 0 2.523 -2.862 0.337
18 O1 O O2 N N N 0 3.165 -3.959 -0.095
19 O O O3 N N N 0 1.599 -2.967 1.109
20 C14 C C13 N Y N 0 2.29 1.45 -1.243
21 N4 N N5 N Y N 0 3.409 3.421 -0.627
22 C12 C C14 N Y N 0 3.611 2.961 0.593
23 C11 C C15 N Y N 0 3.161 1.707 0.96
24 H1 H H1 N N N 0 -6.049 0.743 0.234
25 H6 H H2 N N N 0 -3.102 -1.447 -3.016
26 H7 H H3 N N N 0 -5.064 1.684 2.385
27 H8 H H4 N N N 0 -2.497 1.22 2.345
28 H11 H H5 N N N 0 2.618 3.124 -2.524
29 H5 H H6 N N N 0 0.58 -1.145 -1.042
30 H H H7 N N N 0 1.906 -0.528 1.472
31 H3 H H8 N N N 0 2.957 -1.479 -1.23
32 H4 H H9 N N N 0 3.959 -1.286 0.229
33 H2 H H10 N N N 0 2.852 -4.811 0.239
34 H12 H H11 N N N 0 1.768 0.875 -1.993
35 H10 H H12 N N N 0 4.139 3.57 1.312
36 H9 H H13 N N N 0 3.329 1.337 1.96



A1AKG : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C O C doub 1.21 N N
2 O1 C O C sing 1.34 N N
3 C C1 C C sing 1.51 N N
4 C1 C2 C C sing 1.53 N N
5 C2 N C N sing 1.47 N N
6 N C3 N C sing 1.35 N N
7 C3 O2 C O doub 1.22 N N
8 C4 C3 C C sing 1.48 N N
9 C4 N1 C N doub 1.33 N Y
10 N1 C5 N C sing 1.32 N Y
11 C5 N2 C N doub 1.32 N Y
12 N2 C6 N C sing 1.33 N Y
13 C6 N3 C N sing 1.37 N Y
14 N3 C7 N C sing 1.37 N Y
15 C7 C8 C C doub 1.34 N Y
16 C8 C9 C C sing 1.46 N Y
17 C9 C4 C C sing 1.4 N Y
18 C6 C9 C C doub 1.42 N Y
19 C10 C2 C C sing 1.51 N N
20 C10 C11 C C doub 1.39 N Y
21 C11 C12 C C sing 1.38 N Y
22 C12 N4 C N doub 1.32 N Y
23 N4 C13 N C sing 1.32 N Y
24 C13 C14 C C doub 1.38 N Y
25 C14 C10 C C sing 1.39 N Y
26 N3 H1 N H sing 0.97 N N
27 C5 H6 C H sing 1.08 N N
28 C7 H7 C H sing 1.08 N N
29 C8 H8 C H sing 1.08 N N
30 C13 H11 C H sing 1.08 N N
31 N H5 N H sing 0.97 N N
32 C2 H C H sing 1.09 N N
33 C1 H3 C H sing 1.09 N N
34 C1 H4 C H sing 1.09 N N
35 O1 H2 O H sing 0.97 N N
36 C14 H12 C H sing 1.08 N N
37 C12 H10 C H sing 1.08 N N
38 C11 H9 C H sing 1.08 N N



A1AKG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
A1AKG 7gzd Open in New Window Bound ligand 1 1